<div dir="ltr">Tom,<br>This works beautifully! In the case of the two conformations I'm viewing, it provides very useful information. Thanks again.<br>Joel<br></div><div class="gmail_extra"><br><br><div class="gmail_quote">
On Wed, Jan 29, 2014 at 3:31 PM, Tom Goddard <span dir="ltr"><<a href="mailto:goddard@sonic.net" target="_blank">goddard@sonic.net</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div style="word-wrap:break-word">Hi Joel,
<div><br>
</div>
<div> I don't think surface curvature will be helpful understand the differences between two EM maps. But I was curious what it would look like. So here's a Python script and an image on a simulated map at 15 Angstroms. You use the script by opening your
map, selecting the surface (ctrl-click on it), then open the curvature.py script (menu File / Open…). Here's a description of the method it uses from the comments at the top of the curvature.py file.</div>
<div><br>
</div>
<div>
<div># Color selected surface pieces by mean curvature.</div>
<div>#</div>
<div># Gray at the average curvature value over the surface, and blue and red</div>
<div># at +/- 3 standard deviations of curvature values across the surface.</div>
<div>#</div>
<div># The curvature is estimated from the vertices and normals of the triangulated</div>
<div># surface in simple way which will show artifacts from non-isotropic meshes.</div>
<div># For each triangle edge it computes the normal vector rotation from one vertex</div>
<div># to the other divided by the edge length. The vertex mean curvature is the</div>
<div># mean of the curvatures computed for each edge.</div>
<div>#</div>
</div>
<div><br>
</div>
<div>And the steps to make the example image</div>
<div><br>
</div>
<div><span style="white-space:pre-wrap"></span>open 1grl</div>
<div><span style="white-space:pre-wrap"></span>molmap #0 15 grid 2 model #1</div>
<div><span style="white-space:pre-wrap"></span>select #1</div>
<div><span style="white-space:pre-wrap"></span>open ~/Desktop/curvature.py</div>
<div><br>
</div>
<div> Tom</div>
<div><br>
</div>
<div><br>
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<div></div>
</div>
<div><img src="cid:60e4e299-7c9b-4ec8-9f8e-f370788e9385@mail.nih.gov"> </div>
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<div></div>
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<div><br>
<div>
<div>On Jan 29, 2014, at 9:40 AM, Joel Meyerson wrote:</div>
<br>
<blockquote type="cite"><div class="im">
<div dir="ltr">
<div>Hi Darrell,<br>
Thanks for the tip! I hadn't considered mesh lab but that link you sent looks promising. I'll also wait to see if Tom has any further suggestions.<br>
</div>
Joel<br>
</div>
</div><div><br>
<br>
<div>On Wed, Jan 29, 2014 at 11:44 AM, Hurt, Darrell (NIH/NIAID) [E] wrote:<br>
<blockquote style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word">
<div><div class="im">
<div>Hi Joel,</div>
<div><br>
</div>
<div>I love Chimera and use it all the time. However, a quick-and-dirty solution to your problem might be to try Meshlab. It is kind of buggy software, but can be very useful. Here's a tutorial/blog entry that I found in a quick search. At the very least, it
describes what I think Tom was communicating about enhancing surface shading:</div>
<div><a href="http://meshlabstuff.blogspot.com/2010/03/mean-curvature-cavity-map-zbrush-and.html" target="_blank">http://meshlabstuff.blogspot.com/2010/03/mean-curvature-cavity-map-zbrush-and.html</a></div>
<div><br>
</div>
<div>FWIW,</div>
<div>Darrell</div>
<div><br>
</div>
</div><div><div class="im">
<div><span style="font-size:12px">-- </span></div>
<font><font style="font-size:12px" face="Calibri,Verdana,Helvetica,Arial">Darrell Hurt, Ph.D.<br>
Section Head, Computational Biology<br>
Bioinformatics and Computational Biosciences Branch (BCBB)<br>
OCICB/OSMO/OD/NIAID/NIH<br>
<br>
31 Center Drive, Room 3B62B, MSC 2135<br>
Bethesda, MD 20892-2135<br>
</font></font>
<div><font style="font-size:12px" face="Calibri,Verdana,Helvetica,Arial"><br>
<br>
</font></div>
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<div style="border-width:1pt medium medium;border-style:solid none none;padding:3pt 0in 0in;text-align:left;font-size:11pt;font-family:Calibri;border-top-color:rgb(181,196,223)"><div class="im">
<span style="font-weight:bold">From: </span><Meyerson>, "Joel [F] (NIH/NCI)" <br>
</div><div class="im"><span style="font-weight:bold">Date: </span>Tuesday, January 28, 2014 9:08 PM<br>
<span style="font-weight:bold">To: </span>Tom Goddard <br>
</div><div class="im"><span style="font-weight:bold">Cc: </span>"<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank">chimera-users@cgl.ucsf.edu</a> List" <<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank">chimera-users@cgl.ucsf.edu</a>>
<div><br>
<span style="font-weight:bold">Subject: </span>Re: [Chimera-users] Coloring map by curvature<br>
</div>
</div></div>
<div>
<div>
<div><br>
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<div>
<div><div class="im">
<div dir="ltr">
<div>
<div>Hi Tom,<br>
</div>
I have cryo-EM maps for two conformations of a protein, both in the 15 Angstrom resolution range. The conformations are visibly different, but I am also interested in seeing where they differ in terms of their surface curvature, as it could have bearing on
how I interpret the conformations. If there's any other info I can provide just let me know.<br>
</div>
Thanks!<br>
Joel<br>
</div>
</div><div class="im"><div><br>
<br>
<div>On Tue, Jan 28, 2014 at 7:36 PM, Tom Goddard wrote:<br>
<blockquote style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Joel,<br>
<br>
No, Chimera does not compute surface curvature. It would not be too hard to make a Python script that computed it and used it to color a surface. The main trouble is defining numerically the curvature for a triangulated surface at each vertex. Why are
you interested in this? Is the idea to simulate ambient occlusion lighting where surface cavities are dark and projections are brighter? Is the idea to try it on EM maps or molecular surfaces?<br>
<br>
Tom<br>
<div>
<div><br>
<br>
On Jan 28, 2014, at 2:29 PM, Joel Meyerson wrote:<br>
<br>
> Hi,<br>
> Is it possible to color a map based on surface curvature?<br>
> Thanks,<br>
> Joel<br>
</div>
</div>
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